Pre-Christmas moleclular-clock shenanigans with @sabifo4.bsky.social @mariodosreis.bsky.social @zihengyang.bsky.social

Huge shoutout to the amazing instructor squad @kaplipa.bsky.social , @sabifo4.bsky.social , Tomas Flouri & @zihengyang.bsky.social for smashing another epic #Phylogenomics course! 🚀 Massive thanks to everyone who joined us this week — go crush your data and rock those projects! 💥🔥

Very happy to kick off the 5th edition of the #Phylogenomics course with @kaplipa.bsky.social , Tomas Flouri, @sabifo4.bsky.social , @zihengyang.bsky.social , and a wonderfully diverse cohort of attendees from all around the globe!

Wrapping up our annual joint lab meeting with a visit to the Grant Museum of Zoology at UCL was such a highlight! Always inspiring to reconnect with longtime colleagues, new team members, and collaborators💫

We have had a great time at the Workshop on Computational Genomics at Beijing Normal University! Thank you to all organisers, course assistants, and the fantastic and hard-working participants for making this event possible! 下次见, 谢谢 🌹(1/2)

First up we have Xiyun Jiao and @zihengyang.bsky.social showing the importance of moving beyond model fit testing and embracing sensitivity testing in phylogenetics. In other words, question your data assumptions and test for model robustness not just adequacy. (2/n) doi.org/10.1093/evol...

On measures of influence and discordance in phylogenomic analyses

Abstract. As models are approximate descriptions of real biological processes, and data are collected often with errors and contamination, sensitivity or r

doi.org

Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths. 🔗 doi.org/10.1093/molbev/msaf184 #evobio #molbio

The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model

Abstract. The multispecies coalescent (MSC) model accounts for genealogical fluctuations across the genome and provides a framework for analyzing genomic d

doi.org

In the first Plenary speech of #SMBE2025, Ziheng Yang (@zihengyang.bsky.social) taught us quite a few improbable things on gene flow. We wish you a delicious breakfast for tomorrow, while mulling over these lessons... 😉

Using simulations and empirical data, Thawornwattana, Flouri, @wtf-r-species.bsky.social & @zihengyang.bsky.social ‬ et al. evaluate the performance of the MSC-M model for inferring gene flow. 🔗 doi.org/10.1093/molbev/msaf121 #evobio #molbio #geneflow

Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified

Abstract. Thanks to genomic data, interspecific gene flow is increasingly recognized as a major evolutionary force that shapes biodiversity. Two models hav

doi.org

The first Keynote speech of #SMBE2025 will be given by SMBE's President Ziheng Yang (@zihengyang.bsky.social). "Six impossible things to believe before breakfast, about gene flow" 20.07.2025 | 18h00

What a busy (but sunny) May in Crete!🔆 Ziheng & @sabifo4.bsky.social enjoyed teaching and meeting the participants at the Computational Molecular Evolution course! Ziheng then joined the satellite workshop on Biodiversity Genomics 🌍🧬 Thanks to everyone who made these fantastic meetings possible!!

Congratulations Dr Jiayi Ji!! 🥳Thanks to examiners @hernanaburbano.bsky.social and Simon Martin, now time to enjoy the long weekend! 🎉

And that's a wrap on the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop! Thank you to all the attendees, instructors (@anaserrasilva.bsky.social, @sabifo4.bsky.social, Tomas Flouri and Yuttapong Thawornwattana) and to our wonderful TA @lauramulvey.bsky.social!

The 2nd day of the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop was focused on the Multispecies Coalescent Theory and the usage of BPP, led by our lab members Tomas Flouri and Yuttapong Thawornwattana! 💻🧬

Systematics Association@systassn.bsky.social · last yr.

Day 2 of our (@systassn.bsky.social and SRUK/CERU) joint Bayesian Phylogenetics Workshop is underway! We started with an introduction to the Multispecies Coalescent by Yuttapong Thawornwattana.

The SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop started yesterday! During the 1st day, our lab members Tomas Flouri, @anaserrasilva.bsky.social, and @sabifo4.bsky.social had fun sharing their knowledge on Bayesian statistics, phylogeny inference & timetree inference with the participants💻🧬

Systematics Association@systassn.bsky.social · last yr.

The first joint @systassn.bsky.social and SRUK/CERU Bayesian Phylogenetics Workshop is underway!

Our Workshop on Genomics at Sun Yat-sen University Institute of Advanced Studies Hong Kong has come to an end! We are grateful to all organisers and very pleased to have meet such fantastic and hard-working participants! 下次见, 谢谢 🌹(1/2)

Our lab members @sabifo4.bsky.social, @anaserrasilva.bsky.social, Tomas Flouri, and Yuttapong Thawornwattana are teaching a two-day workshop on Bayesian Phylogenetics Workshop 💻🧬 Pre-register your interest to join this event before March 14th, do not miss the deadline! More details below 🔽

Systematics Association@systassn.bsky.social · last yr.

We are organising an in-person Bayesian Phylogenetics Workshop, in partnership with SRUK/CERU. When: April 29-30, 2025 Where: University College London There are limited places, so please pre-register by March 14th!!! Find more details here: systass.org/workshop-bay...

Thinking of starting a PhD on Bayesian phylogenetics next October 2025 in London? 🎓 You may want to check the TREES project led by the dos Reis Lab on integrating morphology and genomes for timetree inference! 🦴🧬💻Project supervisors: @mariodosreis.bsky.social & Ziheng Yang. More info in link 🔽

Mario dos Reis@mariodosreis.bsky.social · 2y ago

We have a project on Bayesian phylogenetics: www.trees-dla.ac.uk/projects/int... with @zihengyang.bsky.social

Wrapping up an incredible 5-day course on #Phylogenomics with a fascinating lecture on Molecular-Clock dating of species divergence by @mariodosreis.bsky.social, followed by a hands-on session with @sabifo4.bsky.social 🧬🕰️ Huge thanks to all participants for an inspiring week!@zihengyang.bsky.social

Here’s the amazing Phylogenomics Group 2024 📸 Thank you to our incredible instructors for sharing their knowledge and making complex topics approachable and engaging! 🙌 And a big shoutout to all participants—Thanks for joining us this week🎉 @sabifo4.bsky.social @zihengyang.bsky.social

🚨 Exciting Day 3 Ahead! 🚨 Today, we’re honored to have one of the giants of Phylogenomics 🧬✨, @zihengyang.bsky.social, kicking off the day with two lectures on the Multispecies Coalescent Model. Day3 will continue with an hands-on session led by Paschalia Kapli and Tomas Flouri🚀

✨ Day 2 highlight! ✨ Tomas Flouri and @sabifo4.bsky.social delivered masterful lectures and an exceptional hands-on session on Bayesian inference in Phylogenomics. 🎓💡 Their expertise truly shone through! Excited for the insights Day 3 will bring—stay tuned! 🚀

The Physalia Phylogenomics course has started today! Tomas and Paschalia are leading today's session -- now, they are going through the practical session to apply all the concepts they have taught this morning! 💻

Physalia-courses@ONLINE@physaliacourses.bsky.social · 2y ago

Amazing course with an amazing team of instructors. The Phylogenomics course has just started :) @sabifo4.bsky.social @zihengyang.bsky.social

If you have ever wondered whether the PAML documentation could be more interactive... We have good news for you! The PAML GitHub repository has been updated and a fresh PAML Wiki is now available for you to navigate the PAML documentation! 📄💻 (1/n) github.com/abacus-gene/...

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PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, pr...

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Hello BlueSky! The Ziheng Yang Lab will be using this social account to post news about the software we develop, upcoming workshops, and general news in evolutionary biology and computational methods 💻🧬🦴 Keep an eye on this site, we will be posting some news soon!